Helper plasmid argument is required. But in some experiments there is no helper plasmid!

[francesco227]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

Version: 24.10.2 build 5932

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-aav-qc
--bam SQK-NBD114-24_barcode16.bam
--itr1_end 7276
--itr1_start 7149
--itr2_end 8808
--itr2_start 8680
--ref_host sc_genome_new.fa
--ref_rep_cap pMaM816.fasta
--ref_transgene_plasmid pMaM792.fasta
-profile standard

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

I want to run the workflow on data that come from yeast s. cerevisiae in which having an helper plasmid is not required.
The problem is that the helper plasmid argument is required. Also, if run with an empty reference as the helper plasmid argument it returns an error from the samtools indexing.
It would be good to fix this!

Relevant log output

N E X T F L O W   ~  version 24.10.2

Launching `https://github.com/epi2me-labs/wf-aav-qc` [hopeful_turing] DSL2 - revision: bcc199d60a [master]


ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --ref_host

 -- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --ref_helper

 -- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --ref_rep_cap

 -- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --ref_transgene_plasmid

 -- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --itr1_start

 -- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --itr1_end

 -- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --itr2_start

 -- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --itr2_end

 -- Check '.nextflow.log' file for details

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[nrhorner]

Hi @francesco227

Thanks for your feedback. An upcoming release of wf-aav-qc will include the option to supply arbitrary non-transgene plasmid reference files. I will let you know when that is available.